title: rock, second mixing experiment

description: BD Rhapsody

organism:
Homo sapiens
Mus musculus

value: custom single-cell RNA-seq

value: Mix of L-cells and HEK293T cells

value: Mouse adult adipose, human embryonic kidney


title: Pool1 RRMS

status: Public on May 07 2024

type: SRA

city: Donostia

first: Alex

middle: Martínez

last: Ascensión

state: Gipuzkoa

address: P/ Doctor Begiristain

country: Spain

institute: Biogipuzkoa HRI

library_source: transcriptomic

data_processing:
Reads from samples were mapped to human references twice. A first map was performed using GRCh38 (Ensembl version 109) using nf-core/rnaseq v3.12.0 module, with STAR v2.7.9a as mapper. Unmapped reads were again mapped, this time using bowtie2 v2.4.5 with --very-sensitive argument and CHM13 genome version.
Unmapped reads are then mapped using different profilers: kaiju, kraken2, krakenuniq and centrifuge. For each profiler, specific available databases were downloaded or constructed consisting, at least of human, archaeal, bacterial, viral and fungal genomes. After individual profiling was performed, taxpasta v0.3.0 was used to standardise the outputs of each profiler into a common format. Taxa lineages were cut at the genus level.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited file with raw counts per sample

molecule: total RNA

organism: Homo sapiens

source_name: Plasma

extract_protocol:
The concentration and quality of the RNA pools was measured using Bioanalyzer 2100 instrument (Agilent Technologies, Santa Clara, CA, USA) before library preparation at CD Genomics (Shirley, New York, NY, USA). After normalization, rRNA was depleted from the total RNA sample using the Ribo-Zero rRNA removal kit (Illumina, San Diego, CA, USA) and followed by purification and fragmentation steps.
Strand-specific cDNA synthesis was performed, the 3′ ends were adenylated, and adaptors were ligated. The resulting libraries were subjected to standard quality control and normalization processes. Paired-end sequencing was performed with Illumina HiSeq X Ten (Illumina, San Diego, CA, USA), and an average of 40–50 × 10^6 reads were obtained per sample.

tag: tissue

value: Plasma

tag: disease state

value: RRMS

tag: sample type

value: EV


title: Hippocampus, 5xFAD, Vehicle, 1M

city: Irvine

first: Kim

last: Green

state: CA

address: 3400 Biological Sciences III

country: USA

institute: University of California, Irvine

data_processing:
Processing and read map analyses were performed by Novogene Corporation
Assembly: mm10
Supplementary files format and content: .xlsx files contain FPKM for each sample
Supplementary files format and content: .xlsx files contain raw counts for each sample

organism: Mus musculus

source_name: Brain, Hippocampus

extract_protocol:
RNA was extracted using RNA Plus Universal Mini Kit (Qiagen)
RNA Libraries were constructed by Novogene Corporation

value: Brain, Hippocampus

tag: genotype

tag: treatment

value: Vehicle


title: pooled clone sequencing from DNA cloning sample (ENCLB661OJJ)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR744FBH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR744FBH
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB661OJJ

library_source: genomic

data_processing: See GSM*_README.txt supplementary file linked below

molecule: genomic DNA

organism: synthetic construct

source_name: control

value: DNA cloning sample

value: cloning host

tag: biosample encode accession

tag: biosample term name

value: synthetic construct

tag: age

value: 60 days

tag: lab

value: Ryan Tewhey, JAX

tag: Sex

value: not applicable


title: Hippocampus, 5xFAD, Vehicle, 2F


title: pooled clone sequencing from DNA cloning sample (ENCLB310PXD)

description:
https://www.encodeproject.org/experiments/ENCSR772FAR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR772FAR
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB310PXD


title: A549 Ythdc1 ChIP, rep3

city: Pamplona

first: Maite

last: Huarte

state: Navarra

address: c/ Avd Pio XII, 55

institute: Centro de Investigación Médica Aplicada

data_processing:
Alignment: bwa mem
Bigwig obtention: deeptools bamcoverage
Peak-calling: MACS2 --broad --broad-cutoff 0.25 -q 0.1
Assembly: hg19
Supplementary files format and content: Ythdc1.bw: Bigwig obtained with the reads of the ChIP
Supplementary files format and content: Ythdc1_MACS2.bed: Bed file of the peaks detected by MACS2

source_name: Lung adenocarcinoma

growth_protocol: Cells were cultured in DMEM medium (GIBCO), and maintained at 37ºC in presence of 5% CO2

extract_protocol:
30x106 A549 cells were crosslinked with 1% formaldehyde in 1X PBS for 10 minutes in agitation. Crosslinking was quenched with final concentration of 125 mM Glycine (Bio-Rad). Cells were collected and incubated in 7 mL of Cell Lysis Buffer (5 mM Tris [pH 8], 85 mM KCl, 0.5% IGEPAL) for 10 minutes at 4ºC in rotation. Nuclear samples was collected by centrigation for 10 minutes at 3000 xg and 4ºC. Pellet was washed in Cell Lysis Buffer without IGEPAL (5 mM Tris [pH 8], 85 mM KCl) and pelleted again. Pellet was resuspended in RIPA Buffer (150 mM NaCl, 50 mM Tris-HCl [pH 7.5], 0.1% SDS, 0.5% Na-Deoxycholate [Na-DOC], 1% Triton X-100) supplemented with 0.1 mM DTT, 1X cOmplete Protease Inhibitor Cocktail (Roche) and 20U/mL RNAsin Ribonuclease Inhibitors (Promega) for 10 minutes in ice. Lysate was dounced and chromatin was sheared by sonication in a Bioruptor device for 45 cycles (30’’ON-30’’OFF). We cleared nuclear extract by centrifugating 30 minutes at max speed and incubation with 50 µL Protein A/G Dynabeads for 1 hour at 4ºC. Nuclear extract was incubated with primary antibodies (see Table antibodies) overnight at 4ºC in rotation. The following day, 50 µL Protein A/G Dynabeads where washed and mixed to antibody-hybridized nuclear extract for 6 hours at 4ºC. Beads were washed following the next order: 1 wash of Low-Salt Buffer (150 mM NaCl, 20 mM Tris [pH 8], 2 mM EDTA, 0.1% SDS, 1% Triton x-100), 1 wash of High-Buffer (500 mM NaCl, 20 mM Tris [pH 8], 2 mM EDTA, 0.1% SDS, 1% Triton x-100), 1 wash of LiCl Buffer (0.25 M LiCl, 1% IGEPAL, 1% Na-Deoxycholate [Na-DOC], 1 mM EDTA, 10 mM Tris [pH 8]) and 2 washes with TE Buffer (10 mM Tris, 1 mM EDTA [pH 8]). Beads are resuspended in 250 µL of Elution Buffer (25 mM Tris [pH 7.5], 5 mM EDTA, 0.5% SDS) supplemented with 10 µL of 5 M NaCl, 10 µL 1M Tris pH 7, 5 uL 0.5 M EDTA and 20 µg Proteinase K for 4 hours at 65ºC to promote proper decrosslinking of chromatin from immunoprecipitated proteins. DNA was isolated with Phenol:Chloroform:isoamyl (25:24:1) alcohol (Sigma-Aldrich) isolation and quantified by Qubit4 fluorometer (Invitrogen)
Custom protocol

value: Lung adenocarcinoma

tag: cell line


title: pooled clone sequencing from DNA cloning sample (ENCLB840UAS)

description:
https://www.encodeproject.org/experiments/ENCSR813IVZ/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR813IVZ
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB840UAS


title: A549 PolII ChIP, siYTHDC1, rep2

data_processing:
Alignment: bwa mem
Bigwig obtention: deeptools bamcoverage
Assembly: hg19
Supplementary files format and content: PolII_siDC1.bw: bigwig of the pooled reads in siYTHDC1 condition
Supplementary files format and content: PolII_siSCR.bw: bigwig of the pooled reads in siSCR condition

treatment_protocol: For the siSCR and siYTHDC1 knockdowns, siRNAs were transfected 48-72 hours at final concentration of 40 nM. siRNA sequences were obtained from previous studies or designed using the “i-Score Designer” and “siDirect v.2” designing tools, and purchased from Sigma


title: Hippocampus, 5xFAD, Vehicle, 1F


title: pooled clone sequencing from DNA cloning sample (ENCLB792VDS)

description:
https://www.encodeproject.org/experiments/ENCSR798QUP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR798QUP
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB792VDS


title: Hippocampus, 5xFAD, Vehicle, 3F


title: A549 RNAseq, siSCR, rep6

data_processing:
Alignment: STAR
Read count per gene: Htseq-count
Differential gene expression analysis: DESeq2
Assembly: hg19
Supplementary files format and content: siSCR_vs_siDC1_DGA.txt contains the DGA resulting from DESeq2

extract_protocol:
Total RNA was isolated and DNAse I-treated using Maxwell® RSC simplyRNA Tissue kit (Promega), following manufacturer's instructions. 1 µg of RNA was used for library preparation
Truseq Stranded Total RNAseq kit (Illumina) was used after rRNA removal

value: siSCR


title: A549 Ythdc1 ChIP, rep2


title: pooled clone sequencing from DNA cloning sample (ENCLB692VFO)

description:
https://www.encodeproject.org/experiments/ENCSR738NIX/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR738NIX
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB692VFO


title: unmod, first mixing experiment

city: Zürich

first: Giulia

middle: Arianna

last: Moro

address: Winterthurerstrasse 190

department: DMLS

country: Switzerland

institute: University of Zurich

description: BD Rhapsody

library_source: transcriptomic single cell

data_processing:
The mapping, barcode filtering and counting was performed using a custom Snakemake pipeline (https://github.com/imallona/rock_roi_method/) based on STARSolo and featureCounts. Count matrices were analysed in R.
Index the reference genome with STAR.
Subset reads matching the WTA cell barcodes and map those to the transcriptome (genome plus GTF) using STARsolo. Detected cell barcodes (cells) are filtered in at two levels: first, by matching to the user-provided cell barcode whitelist; and second, by applying the EmptyDrops algorithm to discard empty droplets. We report two outputs from this step: the filtered-in cells according to the aforementioned filters; and the unbiased, whole-transcriptome WTA count table
Subset reads matching both the TSO CB structure and the filtered in cell barcodes and map those to the transcriptome. Our reasoning is that the expected TSO transcriptional complexity is undefined and not usable to tell apart cells from empty droplets, so we borrow the filtered-in cells from the EmptyDrops results from the WTA analysis.
(optional) Count on-target features in a more lenient way, filtering in multioverlapping and multimapping reads. This run mode is recommended when the captured regions target non unique loci (i.e. repetitive sequences)
Assembly: Combined genome, mouse: GRCm38.p6.genome.fa and gencode.vM25.annotation.gtf, human: GRCh38.p13.genome.fa and gencode.v38.basic.annotation.gtf. Additional sequences: eGFP and tdTomato
Supplementary files format and content: STARsolo output files wta: tab-delimited tsv and sparse matrix mtx files; filtered by EmptyDrops barcodes (matrix.mtx, barcodes.tsv, features.tsv)
Supplementary files format and content: STARsolo output files tso: tab-delimited tsv and sparse matrix mtx files; raw counts (matrix.mtx, barcodes.tsv, features.tsv)
Supplementary files format and content: tab-delimited featureCounts table for wta for wta and tso (wta_featurecounts.tsv, tso_featurecounts.tsv)
Supplementary files format and content: Bigwig coverage track for wta and tso (tso.bw and wta.bw)
Supplementary files format and content: GTF file containing information on the custom RoCK and ROI regions (custom_regions_mixing.gtf)
Supplementary files format and content: comma-separated table containing information on the species assignment for each cell barcode kept for analysis after doublet removal and QC filtering (species.csv)

source_name: Mix of L-cells and HEK293T cells

growth_protocol: HEK193 cells and L-cells cells were cultured in DMEM 1X with 10% FBS and 1% PIS in a 10 cm dish and maintained in an incubator at 37°C and 5% CO2

extract_protocol:
Cells were dissociated using Trypsin-EDTA, filtered through a cell strainer and resuspended in BD Rhapsody Sample Buffer
Libraries were generated on a BD Rhapsody Express machine. Libraries for unmodified samples (unmod) were generated following manufacturers recommendations for the WTA assay. The protocol for v1 BD Rhapsody was used (i.e. a single RPE reaction) and applied to enhanced beads. The unmod_roi condition was generated following the RoCK and ROI protocol (without addition of the N1 primers). Briefly, the protocol differs from the standard WTA protocol due to the following points: 1) addtion of N1 primer to the RPE PCR (for unmod_n1 condition); 2) separate indexing reaction for the samples in which the N1 primer is added; 3) custom sequencing primer

tag: cell type


title: unmod_T, first mixing experiment

description: BD Rhapsody


title: A549 RNAseq, siSCR, rep4


title: Liver, seamglutide, rep5

city: Lyon

first: Filipe

last: De Vadder

address: 32-34 Avenue Tony Garnier

country: France

institute: Institut de Génomique Fonctionnelle, ENS de Lyon, CNRS UMR5242, Université Claude Bernard Lyon 1

data_processing:
Reads were then analyzed using a local pipeline derived from the one supported by Lexogen.
Adapter sequences were first removed using the Cutadapt package (version 3.5) and quality control of reads was performed using FastQC.
Read mapping was achieved with STAR (Spliced Transcripts Alignment to a Reference, version 2.7.11a) using the Mus musculus GRCm39 genome reference (Ensembl, release 110).
Umi_tools dedup (version 1.1.2) was conducted to UMI deduplication.
The mapped reads were then quantified by htseq-count (version 2.0.3) [34] allowing to generate a count table by sample.
Assembly: GRCm39 (Ensembl, release 110)
Supplementary files format and content: One tsv file for each sample containig raw counts

source_name: liver

growth_protocol: Animals were kept on a low-protein diet for 5 weeks after weaning (5% in kcal).

extract_protocol:
Total RNA was extracted from liver using Nucleospin RNA kit (Macherey-Nagel, 740955.250), following manufacturer's instructions.
For each sample, mRNA purification, based on oligo dT-based mRNA isolation, was conducted with a starting material of 1µg of total RNA using the Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) and following the manufacturer’s instructions. Then, single-indexed libraries were built using the CORALL Total RNA-Seq Library Prep Kit (Lexogen) and following the manufacturer’s instructions.

treatment_protocol: Animals were either treated with vehicle solution (saline) or semaglutide (Novo Nordisk) at 30 nmol/kg of body weight, twice a week.

value: liver

tag: strain

value: WT

value: male

tag: diet

value: low-protein

value: semaglutide


title: Liver, seamglutide, rep2


title: pooled clone sequencing from DNA cloning sample (ENCLB633TSK)

description:
https://www.encodeproject.org/experiments/ENCSR738NIX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR738NIX
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB633TSK


title: A549 RNAseq, siSCR, rep5


title: A549 Ythdc1 ChIP, rep1


title: Hippocampus, WT, D45113, 3M

value: Wild-type (C57BL/6J)


title: pooled clone sequencing from DNA cloning sample (ENCLB913CXR)

description:
https://www.encodeproject.org/experiments/ENCSR738NIX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR738NIX
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB913CXR


title: Hippocampus, WT, D45113, 1M


title: Liver, seamglutide, rep1


title: pooled clone sequencing from DNA cloning sample (ENCLB798ODJ)

description:
https://www.encodeproject.org/experiments/ENCSR738NIX/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR738NIX
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB798ODJ


title: A549 RNAseq, siSCR, rep1


title: A549 RNAseq, siSCR, rep2


title: pooled clone sequencing from DNA cloning sample (ENCLB179ZTV)

description:
https://www.encodeproject.org/experiments/ENCSR720LEA/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR720LEA
assay title: pooled clone sequencing
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB179ZTV


title: Hippocampus, WT, D45113, 4F


title: Liver, vehicle, rep4

value: vehicle


title: Hippocampus, WT, D45113, 4M

value: Brain, Hippocampus


title: pooled clone sequencing from DNA cloning sample (ENCLB476YXT)

description:
https://www.encodeproject.org/experiments/ENCSR720LEA/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR720LEA
assay title: pooled clone sequencing
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB476YXT


title: Hippocampus, WT, D45113, 2M


title: Hippocampus, WT, D45113, 3F


title: A549 RNAseq, siSCR, rep3


title: pooled clone sequencing from DNA cloning sample (ENCLB112EQC)

description:
https://www.encodeproject.org/experiments/ENCSR738NIX/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR738NIX
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB112EQC


title: pooled clone sequencing from DNA cloning sample (ENCLB626IAF)

description:
https://www.encodeproject.org/experiments/ENCSR720LEA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR720LEA
assay title: pooled clone sequencing
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB626IAF


title: Liver, vehicle, rep5


title: Hippocampus, WT, D45113, 2F


title: Liver, seamglutide, rep3


title: Liver, seamglutide, rep4


title: A549 RNAseq, siYTHDC1, rep6


title: pooled clone sequencing from DNA cloning sample (ENCLB886XVR)

description:
https://www.encodeproject.org/experiments/ENCSR720LEA/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR720LEA
assay title: pooled clone sequencing
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB886XVR


title: Liver, vehicle, rep3


title: A549 RNAseq, siYTHDC1, rep5


title: pooled clone sequencing from DNA cloning sample (ENCLB117LUD)

description:
https://www.encodeproject.org/experiments/ENCSR720LEA/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR720LEA
assay title: pooled clone sequencing
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB117LUD


title: A549 RNAseq, siYTHDC1, rep4


title: Hippocampus, 5xFAD, D45113, 4M


title: Liver, vehicle, rep2


title: Hippocampus, WT, D45113, 1F


title: pooled clone sequencing from DNA cloning sample (ENCLB403OQP)

description:
https://www.encodeproject.org/experiments/ENCSR701FXI/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR701FXI
assay title: pooled clone sequencing
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB403OQP


title: Liver, vehicle, rep1


title: Hippocampus, 5xFAD, D45113, 3M


title: Hippocampus, 5xFAD, D45113, 2M


title: A549 RNAseq, siYTHDC1, rep3


title: Tbx18_tdTomato 4

city: New York City

first: Dr. Yu Leng

last: Phua

state: New York

address: 1 Gustave L. Levy Pl

institute: Icahn School of Medicine at Mount Sinai

description:
Wildtype
small RNA-Seq

data_processing:
The Rsubread and limma-voom packages were used for the analysis of the small RNA-Seq data in R.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Tbx18_TPM.txt: Tab-delimited text file includes TPM values for each sample.

source_name: Peri-wolffian duct

extract_protocol:
Tbx18+ cells were FACS sorted directly into QIAzol, and total RNA were extracted using the miRNeasy Micro Kit (Qiagen) in accordance to manufacturer's protocol. The integrity of the RNA was assessed using an Agilent Tapestation prior to library construction.
RNA libraries were prepared for sequencing using the NEBNext Small RNA Library kit.

tag: developmental stage

value: Tbx18-expressing peri-wolffian duct stroma cells


title: Hippocampus, 5xFAD, D45113, 1M


title: pooled clone sequencing from DNA cloning sample (ENCLB161WBX)

description:
https://www.encodeproject.org/experiments/ENCSR701FXI/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR701FXI
assay title: pooled clone sequencing
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB161WBX

value: DNA cloning sample


title: Tbx18_tdTomato 2

description:
Wildtype
small RNA-Seq


title: A549 RNAseq, siYTHDC1, rep2


title: pooled clone sequencing from DNA cloning sample (ENCLB584JNK)

description:
https://www.encodeproject.org/experiments/ENCSR701FXI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR701FXI
assay title: pooled clone sequencing
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB584JNK

value: cloning host


title: Tbx18_tdTomato 3

description:
Wildtype
small RNA-Seq


title: pooled clone sequencing from DNA cloning sample (ENCLB269AMQ)

description:
https://www.encodeproject.org/experiments/ENCSR701FXI/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR701FXI
assay title: pooled clone sequencing
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB269AMQ

value: synthetic construct


title: Hippocampus, 5xFAD, D45113, 4F


title: pooled clone sequencing from DNA cloning sample (ENCLB131FCO)

description:
https://www.encodeproject.org/experiments/ENCSR701FXI/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR701FXI
assay title: pooled clone sequencing
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB131FCO

value: 60 days


title: A549 RNAseq, siYTHDC1, rep1


title: pooled clone sequencing from DNA cloning sample (ENCLB038HNB)

description:
https://www.encodeproject.org/experiments/ENCSR691FFI/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR691FFI
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB038HNB

value: Ryan Tewhey, JAX


title: Hippocampus, 5xFAD, D45113, 3F


title: RNA-Seq KO2 JDP2 repl2

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

country: Germany

institute: Philipps University of Marburg

data_processing:
RNA-Seq data were aligned to human transcriptome GenCode.v43 using RNA Star. Counts per gene were determined using FeatureCounts. Differentially expressed genes and normalized reads were determined using DeSeq2.
Assembly: hg38

growth_protocol: THP1 cells were grown in RPMI Medium 1640 (1X) + GlutaMAX (gibco 61870-010), supplemented with FBS (10% v/v), penicillin (100 units/mL), and streptomycin (100μg/mL).

extract_protocol:
Total RNA was extracted by using the RNeasy Mini system (Qiagen) including an on-column DNaseI digestion.
RNA-Seq libraries were prepared using the Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina.

treatment_protocol: IRF2BP2 knockdown was performed using IRF2BP2 shRNAs in pLKO.1 Vector. ATF7 KO and JDP2 KO cells were obtained upon transfection with the respective Lenti-CRISPRv2 constructs. Single cell clones were obtained via limited dilution.

value: AML cell line

value: JDP2 KO (Clone 2)


title: RNA-Seq KO2 JDP2 repl1


title: RNA-Seq KO1 JDP2 repl2

value: JDP2 KO (Clone 1)


title: Hippocampus, 5xFAD, D45113, 2F


title: Hippocampus, 5xFAD, D45113, 1F


title: RNA-Seq KO1 JDP2 repl1


title: RNA-Seq KO2 ATF7 repl2

value: ATF7 KO (Clone 2)


title: pooled clone sequencing from DNA cloning sample (ENCLB162FKC)

description:
https://www.encodeproject.org/experiments/ENCSR691FFI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR691FFI
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB162FKC

value: not applicable


title: HEK_CloneZD29_30min_dTAGV1_PRO-seq rep2

city: Farmington

first: Jinhong

last: Dong

state: CT

address: 400 Farmington Ave

department: Center for Cell Analysis and Modeling

institute: University of Connecticut

description:
HEK_CloneZD29_30min_dTAGV1_minus_PE1_scaled.bigWig
HEK_CloneZD29_30min_dTAGV1_minus_PE2_scaled.bigWig
HEK_CloneZD29_30min_dTAGV1_plus_PE1_scaled.bigWig
HEK_CloneZD29_30min_dTAGV1_plus_PE2_scaled.bigWig

data_processing:
*library strategy: PRO-seq
Adapter trimming: cutadapt v3.5
FASTQ deduplication:https://github.com/guertinlab/fqdedupv1.0.0
FASTQ pairing: fastq_pair v1.0
UMI trimming and reverse complementing: fastX-trimmer and seqtk v1.3
Alignment: bowtie2
File manipulation: samtools v1.9
File manipulation: https://github.com/guertinlab/seqOutBias v1.4.0
Assembly: hg38
Supplementary files format and content: Stranded bigWig counts files

extract_protocol:
Cell permeabilization was performed as previously described (Mahat et al. 2016), with modifications. At the time of harvest, cells were scraped in 10mL ice cold PBS and washed in 5mL buffer W (10mM Tris-HCl pH 7.5, 10mM KCl, 150mM sucrose, 5mM MgCl2, 0.5mM CaCl2, 0.5mM DTT, 0.004U/mL SUPERaseIN RNase inhibitor (Invitrogen), Complete protease inhibitors (Roche)). Cells were permeabilized by incubating with buffer P (10 mM Tris-HCl pH 7.5, KCl 10 mM, 250 mM sucrose , 5 mM MgCl2, 1 mM EGTA, 0.05% Tween-20, 0.1% NP40, 0.5 mM DTT, 0.004 units/mL SUPERaseIN RNase inhibitor (Invitrogen), Complete protease inhibitors (Roche)) for 3 minutes on ice. Cells were washed with 10 mL buffer W before being transferred into 1.5mL tubes using wide bore pipette tips. Finally, cells were resuspended in 50μL buffer F (50mM Tris-HCl pH 8, 5mM MgCl2, 0.1mM EDTA, 50% Glycerol, 0.5 mM DTT). Cells were snap frozen in liquid nitrogen and stored at -80°C.
PRO-seq libraries were prepared as previously described (Judd et al. 2020), with modifications. RNA extraction after the run-on reaction was performed with 500μL Trizol LS (Thermo Fisher) followed by 130μL chloroform (Sigma). The equivalent of 1μL of 50μM for each adapter was used. A random eight base unique molecular identifier (UMI) was included at the 5′ end of the adapter ligated to the 3′ end of the nascent RNA. 37°C incubations were performed with rotation with 1.5mL tubes placed in 50mL conical tubes in a hybridization oven. For the reverse transcription reaction, RP1 was used at 100μM and dNTP mix was used at 10mM each. Libraries were amplified by PCR for a total of 8 cycles in 100μL reactions with Phusion polymerase (New England Biolabs). No PAGE purification was performed to ensure that our libraries were not biased against short nascent RNA insertions.

treatment_protocol: HEK-293T cells were collected after either no treatment or after 30 minutes of 50nm dTAGV-1 treatment

value: ZNF143 tagged with an inducible degron tag

value: 50nM dTAG-V-1 for 30 minutes

tag: molecule subtype

value: nascent RNA


title: HEK_CloneZD29_30min_dTAGV1_PRO-seq rep3


title: HEK_CloneZD29_30min_dTAGV1_PRO-seq rep4


title: pooled clone sequencing from DNA cloning sample (ENCLB243DPX)

description:
https://www.encodeproject.org/experiments/ENCSR691FFI/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR691FFI
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB243DPX


title: Tbx18_tdTomato 1

description:
Wildtype
small RNA-Seq


title: RNA-Seq KO2 ATF7 repl1


title: pooled clone sequencing from DNA cloning sample (ENCLB219FKR)

description:
https://www.encodeproject.org/experiments/ENCSR691FFI/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR691FFI
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB219FKR


title: HEK_CloneZD29_30min_dTAGV1_PRO-seq rep1


title: RNA-Seq KO1 ATF7 repl2

value: ATF7 KO (Clone 1)


title: pooled clone sequencing from DNA cloning sample (ENCLB120WPV)

description:
https://www.encodeproject.org/experiments/ENCSR691FFI/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR691FFI
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB120WPV


title: TT3/ Tipifarnib treated TAC 3

city: Philadelphia

first: Vandana

last: Mallaredy

state: Pennsylvania

address: 3500 N Broad St, MERB 983

department: Aging + Cardiovascular Discovery Center

institute: Temple University

description: Small RNA sequence for serum extracellular vesicles

data_processing:
next-generation sequencing using an Illumina NovaSeq platform and 2x150bp paired-end reads.
~350M raw paired-end reads per lane
FASTQ files, data QC, trimming, mapping, differential small RNA expression analysis, and novel small RNA discovery
DEseq was used to analyze the differentially expressed genes (DEG) for samples with biological replicates.
Fold change ≥2 and FDR>0.05 were set as screening criteria. miRNAs enrichment analyses of upregulated and downregulated genes were performed using KEGG and GO databases.
Assembly: not provided
Supplementary files format and content: Excel Workbook

source_name: Serum

growth_protocol: No culture - Serum used

extract_protocol:
RNA was extracted using Rneasy mini kit (Qiagen), â‰¥2µg  total RNA was used for the construction of the sequencing library
Illumina mRNA seq TruSeq
Small RNA-Seq uses kits that specifically recognize the 5' and 3' ends of RNA after processing by DICER

treatment_protocol: Tipifarnib 10mg/kg body weight of mice and TAC surgery

value: Serum

value: Extracellular vesicles

value: WT

value: Male

value: Tipifarnib treated TAC


title: HEK_CloneZD29_30min_control_PRO-seq rep4

description:
HEK_CloneZD29_30min_control_minus_PE1_scaled.bigWig
HEK_CloneZD29_30min_control_minus_PE2_scaled.bigWig
HEK_CloneZD29_30min_control_plus_PE1_scaled.bigWig
HEK_CloneZD29_30min_control_plus_PE2_scaled.bigWig

value: no treatment


title: TT2/ Tipifarnib treated TAC 2


title: pooled clone sequencing from DNA cloning sample (ENCLB339GVA)

description:
https://www.encodeproject.org/experiments/ENCSR686UKL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR686UKL
assay title: pooled clone sequencing
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB339GVA

value: DNA cloning sample

value: cloning host

value: synthetic construct

value: 60 days


title: TT1/ Tipifarnib treated TAC 1


title: HEK_CloneZD29_30min_control_PRO-seq rep3


title: RNA-Seq KO1 ATF7 repl1

value: AML cell line


title: T3/ TAC 3

value: TAC


title: T2/ TAC 2


title: RNA-Seq KO Control repl2

value: KO Control


title: RNA-Seq KO Control repl1


title: pooled clone sequencing from DNA cloning sample (ENCLB612WKA)

description:
https://www.encodeproject.org/experiments/ENCSR652NKB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR652NKB
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB612WKA

value: Ryan Tewhey, JAX

value: not applicable


title: HEK_CloneZD29_30min_control_PRO-seq rep1

value: ZNF143 tagged with an inducible degron tag

value: nascent RNA


title: HEK_CloneZD29_30min_control_PRO-seq rep2


title: T1/ TAC 1

value: Serum


title: HEK293T_DTAG_ATAC-seq rep8

data_processing:
Adapter trimming: cutadapt v1.8.1
UMI trimming and reverse complementing: seqtk v1.3
FASTQ deduplication:https://github.com/guertinlab/fqdedupv1.0.0
FASTQ pairing: fastq_pair v1.0
Alignment: bowtie2 v2.4.4
File manipulation: samtools v1.9
File manipulation:https://github.com/guertinlab/seqOutBiasv1.3.1
Assembly: hg38
Supplementary files format and content: bigWig counts files
Supplementary files format and content: peak summit counts files

extract_protocol:
At the time of harvest, cells were moved to ice and scraped in 1mL ice cold PBS, and 100μL (∼5 x 10^4 cells) were transferred to 1.5 mL tubes. Cells were centrifuged at 500 x g for 5 minutes at 4°C, and the pellets were resuspended in 50 μL cold lysis buffer (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2, 0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin, adjusted to pH 7.4) and incubated on ice for 3 minutes. Samples were washed with 1 mL cold wash buffer (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2, 0.1% Tween-20). Cells were centrifuged at 500 x g for 10 minutes at 4°C, and pellets were resuspended in the transposition reaction mix (25 μL 2X TD buffer (Illumina), 2.5 μL TDE1 Tn5 transposase (Illumina), 16.5 μL PBS, 0.5 μL 1% Digitonin, 0.5 μL 10% Tween-20, 5 μL nuclease-free water) and incubated in a thermomixer at 37°C and 100rpm for 30 minutes. DNA was extracted with the DNA Clean and Concentrator-5 Kit (Zymo Research).
Sequencing adapters were attached to the transposed DNA fragments using NEBNext Ultra II Q5 PCR mix (New England Biolabs), and libraries were amplified with 8 cycles of PCR. PEG-mediated size fractionation (Lis 1980) was performed on the libraries by mixing SPRIs-elect beads (Beckman) with each sample at a 0.5:1 ratio, then placing the reaction vessels on a magnetic stand. The right side selected sample was transferred to a new reaction vessel, and more beads were added for a final ratio of 1.8:1. The final size-selected sample was eluted into nuclease-free water. This size selection protocol was repeated to further remove large fragments.

value: 50nm dTAGV-1 treatment


title: pooled clone sequencing from DNA cloning sample (ENCLB006RFS)

description:
https://www.encodeproject.org/experiments/ENCSR645FSB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR645FSB
assay title: pooled clone sequencing
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB006RFS


title: S3/Sham 3

value: Extracellular vesicles

value: WT

value: Sham


title: S2/Sham 2

value: Male


title: pooled clone sequencing from DNA cloning sample (ENCLB167IGZ)

description:
https://www.encodeproject.org/experiments/ENCSR645FSB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR645FSB
assay title: pooled clone sequencing
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB167IGZ

value: DNA cloning sample


title: RNA-Seq WT repl1 (low quality)


title: pooled clone sequencing from DNA cloning sample (ENCLB451PGE)

description:
https://www.encodeproject.org/experiments/ENCSR645FSB/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR645FSB
assay title: pooled clone sequencing
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB451PGE

value: cloning host


title: HEK293T_DTAG_ATAC-seq rep7


title: RNA-Seq shRNA2 IRF2BP2 repl3

value: shRNA2 IRF2BP2


title: RNA-Seq WT repl2


title: S1/Sham 1


title: RNA-Seq shRNA2 IRF2BP2 repl2


title: pooled clone sequencing from DNA cloning sample (ENCLB652SYI)

description:
https://www.encodeproject.org/experiments/ENCSR631SLY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR631SLY
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB652SYI

value: synthetic construct

value: 60 days


title: pooled clone sequencing from DNA cloning sample (ENCLB924GCA)

description:
https://www.encodeproject.org/experiments/ENCSR633PMZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR633PMZ
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB924GCA


title: HEK293T_DTAG_ATAC-seq rep5


title: HEK293T_DTAG_ATAC-seq rep4


title: Colon, rockroi unimodal

description:
BD Rhapsody
custom_regions_pdgfra.gtf.gz

data_processing:
The mapping, barcode filtering and counting was performed using a custom Snakemake pipeline (https://github.com/imallona/rock_roi_method/) based on STARSolo and featureCounts. Count matrices were analysed in R.
Index the reference genome with STAR.
Subset reads matching the WTA cell barcodes and map those to the transcriptome (genome plus GTF) using STARsolo. Detected cell barcodes (cells) are filtered in at two levels: first, by matching to the user-provided cell barcode whitelist; and second, by applying the EmptyDrops algorithm to discard empty droplets. We report two outputs from this step: the filtered-in cells according to the aforementioned filters; and the unbiased, whole-transcriptome WTA count table
Subset reads matching both the TSO CB structure and the filtered in cell barcodes and map those to the transcriptome. Our reasoning is that the expected TSO transcriptional complexity is undefined and not usable to tell apart cells from empty droplets, so we borrow the filtered-in cells from the EmptyDrops results from the WTA analysis.
(optional) Count on-target features in a more lenient way, filtering in multioverlapping and multimapping reads. This run mode is recommended when the captured regions target non unique loci (i.e. repetitive sequences)
Assembly: Combined genome, mouse: GRCm38.p6.genome.fa and gencode.vM25.annotation.gtf. Additional sequences: eGFP, and custom sequences of mouse strain
Supplementary files format and content: STARsolo output files wta: tab-delimited tsv and sparse matrix mtx files; filtered by EmptyDrops barcodes (matrix.mtx, barcodes.tsv, features.tsv)
Supplementary files format and content: STARsolo output files tso: tab-delimited tsv and sparse matrix mtx files; raw counts (matrix.mtx, barcodes.tsv, features.tsv)
Supplementary files format and content: tab-delimited featureCounts table for wta for wta and tso (wta_featurecounts.tsv, tso_featurecounts.tsv)
Supplementary files format and content: Bigwig coverage track for wta and tso (tso.bw and wta.bw)
Supplementary files format and content: GTF file containing information on the custom RoCK and ROI regions (custom_regions_pdgfra.gtf)
Supplementary files format and content: comma-separated table containing information on the broad cell (mesenchymal vs epithelial) and cluster annotation for each cell barcode kept for analysis after doublet removal and QC filtering (annotation.csv)
Library strategy: custom scRNAseq

source_name: Colon

extract_protocol:
Murine colonic tissues from Pdgfra-H2B-EGFP reporter mice (Hamilton et al., 2003) were flushed with PBS and finely minced into 2 mm pieces. Minced tissue fragments were washed three times with PBS. For the detachment of the epithelial fraction, the tissue pieces were incubated in Gentle Cell Dissociation Reagent (STEMCELL Technologies, Germany) while gently rocking for 30 minutes at room temperature. The pieces were pipetted up and down for the epithelial fraction to be detached. The epithelial fraction was filtered through a Falcon 70-μm cell strainer (Corning, Switzerland), washed with plain ADMEM/F12 and incubated for 5 minutes at 37°C in prewarmed TrypLE express (Gibco, Thermofisher, Switzerland). The gentleMACS Octo Dissociator (Miltenyi Biotec, Switzerland) m_intestine program was employed for single-cell dissociation. The obtained epithelial single-cell suspension was filtered through a Falcon 40-μm cell strainer (Corning) and kept on ice in ADMEM/F12 supplemented with 10% FBS. For dissociation of the mesenchymal fraction, the remaining tissue pieces (following epithelium detachment) were digested for 1 hour at 37°C under 110 revolutions per minute (rpm) shaking conditions in DMEM supplemented with 2 mg/mL collagenase D (Roche) and 0.4 mg/mL Dispase (Gibco). The mesenchymal fraction was filtered through a Falcon 70-μm cell strainer (Corning), washed with plain ADMEM/F12, and subsequently filtered through a Falcon 40-μm cell strainer (Corning). The epithelial and mesenchymal cells were mixed and stained for 30 minutes on ice with anti-CD326(EpCAM)-PE-Cy5 (1:500, eBioscience/Thermofisher, Switzerland) in PBS. Prior to cell sorting, all cells were stained for 5 minutes on ice with DAPI in PBS (1:1000, ThermoFisher, Switzerland). Epithelial and mesenchymal cells labeled with PE-Cy5 and EGFP were sorted separately and subsequently mixed in a 1:1 ratio. Cells were sorted at the Cytometry Facility at the University of Zürich using a FACSAria III cell sorter (BD Biosciences, Switzerland).
Libraries were generated on a BD Rhapsody Express machine. Libraries for unmodified samples were generated following manufacturers recommendations for the WTA assay. The protocol for v1 BD Rhapsody was used (i.e. a single RPE reaction) and applied to enhanced beads. The RoCK and ROI sample was generated following the RoCK and ROI protocol. Briefly, the protocol differs from the standard WTA protocol due to the following points: 1) addtion of N1 primer to the RPE PCR; 2) addition of ROIseq primers to the pool of randomeres during RPE extension; 3) separate indexing reaction for the samples in which the N1 primer is added; 4) custom sequencing primer

tag: protocol

value: custom single-cell RNA-seq

value: Colon

value: Epithelial, Pdgfra positive fibroblasts


title: pooled clone sequencing from DNA cloning sample (ENCLB858EYE)

description:
https://www.encodeproject.org/experiments/ENCSR620BYE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR620BYE
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB858EYE

value: Ryan Tewhey, JAX

value: not applicable


title: pooled clone sequencing from DNA cloning sample (ENCLB340BZM)

description:
https://www.encodeproject.org/experiments/ENCSR645FSB/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR645FSB
assay title: pooled clone sequencing
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB340BZM


title: HEK293T_DTAG_ATAC-seq rep3

value: ZNF143 tagged with an inducible degron tag


title: RNA-Seq shRNA1 IRF2BP2 repl2

value: AML cell line

value: shRNA1 IRF2BP2


title: Colon, unmod unimodal

tag: tissue


title: pooled clone sequencing from DNA cloning sample (ENCLB214NXD)

description:
https://www.encodeproject.org/experiments/ENCSR607LDI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR607LDI
assay title: pooled clone sequencing
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB214NXD


title: RNA-Seq shRNA1 IRF2BP2 repl3


title: Colon, rockroi multimodal


title: HEK293T_DTAG_ATAC-seq rep2

value: 50nm dTAGV-1 treatment


title: NC GEMM mouse #2, tumor

city: East Lansing

first: Bin

last: Gu

state: MI

address: 755 Woodlot Drive

department: OBGYN

institute: Michigan State University

description:
K140424100..Delly.SV.filtered.vcf
K140424100_pass_filtered_robustS_rmSNP_header_eff_SNP.vcf

data_processing:
The trimmed reads were aligned to the GENCODE mouse primary genome assembly (GRCm39, release M32) using the BWA-MEM algorithm in the Burrows-Wheeler Aligner (BWA) v0.7.17 with following options: -M to flag shorter split hits as secondary; -R to add read group information.
The SortSam tool of Picard v2.25.0 was used to sort the output files from BWA by queryname and export output as binary Sam (BAM) files.  Subsequently, duplicate reads were marked using markDuplicates tool in Picard and the resulting files were sorted using SortSam by coordinates.
The Mutect2 tool of GATK v4.1.4.1 used to identify and call variants in each sample individually. Variants were firstly filtered using FilterMutectCalls of GATK to remove probable technical or germline artifacts. Additional filters can be used to decrease the false-positive rate via SnpSift v4.1: mutant allele frequency (≥5%), coverage at particular positions in tumor and normal samples (≥5×) and supporting reads for the mutation in the tumor samples (at least two). Filtered variants were further compared to exclude known polymorphisms by using bcftools v1.9.64.  snpEff v4.1 was used to annotate the effects of variants.
Large structural variations were identified using Delly v0.7.8 with default parameters and then filtered to get a set of confident somatic structural variants by using the following sets: -f somatic -a 0.1 -m 400 -p.
Assembly: GRCm39/mm39
Supplementary files format and content: vcf files include variants and structural variations for each sample
Library strategy: WGS

source_name: tumor

extract_protocol:
Genomic DNAs was extracted from normal and tumor samples using The GeneJet DNA kit (Thermo Fisher), according to the manufacturer’s instructions.
The quality control, library preparation (NEB Next Ultra II for DNA Library Prep kit) and whole genomic sequencing (WGS) were performed by Novogene Inc. following standard protocol. A total of 1.0 ug DNA per sample was used for library preparations. Each sample was sequenced for 10-16 X coverage

value: tumor

value: KRT14Cre+/-;Brd4loxp/wt; Nutm1loxp/wt


title: RNA-Seq shRNA1 IRF2BP2 repl1


title: pooled clone sequencing from DNA cloning sample (ENCLB961SMW)

description:
https://www.encodeproject.org/experiments/ENCSR556IED/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR556IED
assay title: pooled clone sequencing
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB961SMW


title: HEK293T_DTAG_ATAC-seq rep1


title: pooled clone sequencing from DNA cloning sample (ENCLB540NKZ)

description:
https://www.encodeproject.org/experiments/ENCSR556IED/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR556IED
assay title: pooled clone sequencing
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB540NKZ


title: RNA-Seq shRNA Control repl3

value: shRNA Control


title: HEK293T_DTAG_ATAC-seq rep6


title: HEK293T_DMSO_ATAC-seq rep8


title: HEK293T_DMSO_ATAC-seq rep7


title: RNA-Seq shRNA2 IRF2BP2 repl1


title: RNA-Seq shRNA Control repl2 (low quality)


title: NC GEMM mouse #1, tumor

description:
K140411001.Delly.SV.filtered.vcf
K140411001_pass_filtered_robustS_rmSNP_header_eff_SNP.vcf


title: pooled clone sequencing from DNA cloning sample (ENCLB462UXH)

description:
https://www.encodeproject.org/experiments/ENCSR556IED/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR556IED
assay title: pooled clone sequencing
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB462UXH

value: DNA cloning sample


title: pooled clone sequencing from DNA cloning sample (ENCLB693CPH)

description:
https://www.encodeproject.org/experiments/ENCSR556IED/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR556IED
assay title: pooled clone sequencing
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB693CPH

value: cloning host


title: RNA-Seq shRNA Control repl1


title: NC GEMM mouse #1, liver

value: liver


title: normal_oral_mucosa_6

data_processing:
Quality trimmed reads were pseudoaligned to GENCODE mouse transcript reference (GRCm39, release M32) and transcription levels were quantified using kallisto
Differential expression analysis were carried out using the Bioconductor v3.17.1 package DESeq2 v1.40.2
Assembly: GRCm39/mm39
Supplementary files format and content: tab-delimited text files incudes raw counts and normalized counts (median of ratios methods) for each sample

molecule: polyA RNA

source_name: normal oral mucosa

extract_protocol:
Total RNA was prepared from tumors and normal tissues using the RNeasy Mini Kit (Qiagen Inc.).
The quality control, cDNA library preparationpreparation (using NEBNext Ultra™ II RNA Library Prep Kit for Illumina) and bulk RNA sequencing were performed by Novogene Inc. following standard protocol using the Novaseq 6000 sequencer.

value: normal oral mucosa

value: Brd4loxp/wt; Nutm1loxp/wt


title: HEK293T_DMSO_ATAC-seq rep6


title: pooled clone sequencing from DNA cloning sample (ENCLB794IAQ)

description:
https://www.encodeproject.org/experiments/ENCSR556IED/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR556IED
assay title: pooled clone sequencing
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB794IAQ

value: synthetic construct

value: 60 days


title: pooled clone sequencing from DNA cloning sample (ENCLB008QII)

description:
https://www.encodeproject.org/experiments/ENCSR517VAN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR517VAN
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB008QII
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500


title: normal_oral_mucosa_4


title: normal_oral_mucosa_5


title: HEK293T_DMSO_ATAC-seq rep4


title: pooled clone sequencing from DNA cloning sample (ENCLB652FYD)

description:
https://www.encodeproject.org/experiments/ENCSR482UPX/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR482UPX
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB652FYD


title: HEK293T_DMSO_ATAC-seq rep3


title: NC GEMM mouse #2, liver


title: pooled clone sequencing from DNA cloning sample (ENCLB244ODI)

description:
https://www.encodeproject.org/experiments/ENCSR482UPX/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR482UPX
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB244ODI


title: HEK293T_DMSO_ATAC-seq rep2


title: pooled clone sequencing from DNA cloning sample (ENCLB825IKZ)

description:
https://www.encodeproject.org/experiments/ENCSR482UPX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR482UPX
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB825IKZ


title: normal_oral_mucosa_1


title: normal_oral_mucosa_2


title: HEK293T_DMSO_ATAC-seq rep1


title: mock-dTAG-rep2

data_processing:
Adapter trimming: cutadapt
Alignment: bowtie2
File manipulation: samtools v1.16.1
File manipulation: https://github.com/guertinlab/seqOutBias v1.4.0
Peak calling: macs3
File manipulation: bedtools
Assembly: hg38
Supplementary files format and content: bigWig counts files
Supplementary files format and content: peak summit counts files

growth_protocol: HEK293T-ZNF143-dTAG cells were cultured in DMEM (Gibco) supplemented with 10% fetal bovine serum (R&D Systems), 1% L-glutamine (Gibco), 1% sodium pyruvate (Gibco), and 1% penicillin-streptomycin (Gibco).

extract_protocol:
After treatment, cells were fixed with 1% formaldehyde for 10 minutes at 37°C and quenched with 125mM Glycine (Fisher) for 10 minutes at 37°C. Plates were moved to ice, and cells were washed and scraped into ice cold PBS containing Complete EDTA-free Protease Inhibitor Cocktail (Roche). Cells were pelleted in aliquots of 2*10^7 cells, snap frozen in liquid nitrogen, and stored at -80°C. Pellets were thawed, and cells were lysed in 1mL ChIP Lysis Buffer (0.5% SDS, 10mM EDTA, 50mM Tris-HCL pH 8.0), with protease inhibitor cocktail added fresh, for 10 minutes with rotation at 4°C. Lysates were sonicated at 70% amplitude for 15 seconds on and 45 seconds off for 4 sets of 20-minute cycles. Sonicated lysates were moved to 1.5ml tubes and clarified by centrifugation at 14,000rpm for 10 min in 4°C. 50μL of the supernatant was diluted into 760μL ChIP Dilution Buffer (0.01% SDS, 1.1% Triton X-100, 1.2mM EDTA, 167mM NaCl, 16.6mM Tris-HCl pH 8.0), with protease inhibitor cocktail added fresh (1*10^6 cells in 200μL). 1ml (4*106 cells) was aliquoted into each of 3 tubes with antibody (2μg anti-HA  Invitrogen REF 26183, 8μg anti-SP1 Santa Cruz Biotechnology sc-17824 X, or mock IP), and incubated with end-over-end rotation at 4°C overnight. 80μL Protein A/G Magnetic Beads (New England Biolabs) per sample were washed with bead washing buffer (PBS with 0.1% BSA and 2mM EDTA) and then incubated with samples for 90 minutes with rotation at 4°C. The samples were washed once each with low salt immune complex buffer (0.1% SDS, 1% Triton x-100, 2mM EDTA, 150mM NaCl, 20mM Tris HCl pH8.0), high salt immune complex buffer (0.1% SDS, 1% Triton x-100, 2mM EDTA, 500mM NaCl, 20mM Tris Hcl pH 8.0), LiCl immune complex buffer (0.25M LiCl, 1% NP-40, 1% deoxycholate, 1mM EDTA, 10mM Tris-HCl pH8.0), and 1xTE (10mM Tris-HCl, 1mM EDTA pH8.0). Immune complexes were eluted in elution solution, (1% SDS, 0.1M sodium bicarbonate). 1μl RNase A was added to each sample for 10 min at 37°C. Proteins were digested with the addition of 5μl Proteinase K and incubated in a 65°C water bath overnight.
DNA was purified with a MinElute PCR purification kit (Qiagen), and libraries were prepared with a NEBNext Ultra II Library Prep Kit (New England Biolabs).

treatment_protocol: HEK-293T cells were harvested after either no treatment or after 30 minutes of 50nm dTAGV-1 treatment


title: mNC_tumor 6

source_name: oral mNC tumor

value: oral mNC tumor


title: pooled clone sequencing from DNA cloning sample (ENCLB726JHV)

description:
https://www.encodeproject.org/experiments/ENCSR482UPX/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR482UPX
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB726JHV

value: Ryan Tewhey, JAX


title: pooled clone sequencing from DNA cloning sample (ENCLB027KJP)

description:
https://www.encodeproject.org/experiments/ENCSR482UPX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR482UPX
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB027KJP

value: not applicable


title: mNC_tumor 5


title: mNC_tumor 3


title: mock-control-rep2

value: ZNF143 tagged with an inducible degron tag


title: pooled clone sequencing from DNA cloning sample (ENCLB993PER)

description:
https://www.encodeproject.org/experiments/ENCSR441MQR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR441MQR
assay title: pooled clone sequencing
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB993PER


title: mock-dTAG-rep1


title: mNC_tumor 4


title: pooled clone sequencing from DNA cloning sample (ENCLB158VJF)

description:
https://www.encodeproject.org/experiments/ENCSR441MQR/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR441MQR
assay title: pooled clone sequencing
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB158VJF


title: pooled clone sequencing from DNA cloning sample (ENCLB881RPL)

description:
https://www.encodeproject.org/experiments/ENCSR471OZH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR471OZH
assay title: pooled clone sequencing
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB881RPL


title: HEK293T_DMSO_ATAC-seq rep5


title: antiZNF143-dTAG-rep2

description:
antiZNF143-dTAG_merged_normalized.bigWig
antiZNF143_ChIP2_summits.bed


title: normal_oral_mucosa_3


title: pooled clone sequencing from DNA cloning sample (ENCLB453GNE)

description:
https://www.encodeproject.org/experiments/ENCSR441MQR/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR441MQR
assay title: pooled clone sequencing
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB453GNE


title: pooled clone sequencing from DNA cloning sample (ENCLB177AVF)

description:
https://www.encodeproject.org/experiments/ENCSR441MQR/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR441MQR
assay title: pooled clone sequencing
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB177AVF


title: pooled clone sequencing from DNA cloning sample (ENCLB782IJV)

description:
https://www.encodeproject.org/experiments/ENCSR441MQR/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR441MQR
assay title: pooled clone sequencing
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB782IJV


title: antiZNF143-control-rep2

description:
antiZNF143-control_merged_normalized.bigWig
antiZNF143_ChIP2_summits.bed


title: antiZNF143-control-rep1


title: neonate_d14

city: Vienna

first: Jingkui

last: Wang

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology (IMP)

data_processing:
First, 10x Visium raw FASTQ data of the neonatal heart collected at day1, day4, day7 and day14 after injury were processed and mapped using SpaceRanger (v1.3.0) by manually aligning corresponding H&E images.
The reference genome mm10 (i.e., refdata-mm10_gex.10x.2020.A) from SpaceRanger was utilized. Subsequently, for each time point, the filtered feature barcode matrix and the associated image were imported into Seurat (v4.1.1).
Furthermore, the images were cropped manually to preserve only the Visium spots that cover heart tissue and Visium spots with less than 500 UMIs or less than 300 detected genes were filtered out.
Finally, individual time point were normalized using the SCTransform method (sctransform v0.3.4) with 3000 variable genes before all time points were merged into one single Seurat object.
Assembly: mm10
Supplementary files format and content: matrix.mtx.gz: gene expression count data
Supplementary files format and content: barcodes.tsv.gz: a list of spatial barcodes
Supplementary files format and content: features.tsv.gz: a list of gene IDs
Supplementary files format and content: .tif :  tissue H&E images

source_name: Heart

extract_protocol:
Fresh frozen tissue were embbeded in OCT and 10um sections were cut with cryostat
According to 10x genomics Visium protocols

treatment_protocol: Cryoinjury was induced by pre-cooled cryoprobe attached to the apex of the heart's left ventricle for 5 seconds. Post natal day 1 ICR mice were anesthetized by cooling on an ice bed for 3 minutes. Lateral thoracotomy was performed at the third intercostal space by piercing with forceps and then replacing with blunt end forceps. Pushing gently on the belly pushes out the heart making it exposed for cryoinjury. Following the cryoinjury the heart is pushed back to the chest cavity, all surgical tools removed and chest cavity is closed by suture and moved to recovery.

value: Heart

value: Heart cells

tag: time point

value: Cryo injury


title: pooled clone sequencing from DNA cloning sample (ENCLB090BSU)

description:
https://www.encodeproject.org/experiments/ENCSR437KIU/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR437KIU
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB090BSU


title: neonate_d7


title: antiSP1-dTAG-rep3

description:
antiSP1-dTAG_merged_normalized.bigWig
antiSP1_ChIP_summits_final.bed

value: 50nm dTAGV-1 treatment


title: neonate_d4


title: neonate_d1


title: pooled clone sequencing from DNA cloning sample (ENCLB958QGW)

description:
https://www.encodeproject.org/experiments/ENCSR437KIU/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR437KIU
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB958QGW


title: antiSP1-dTAG-rep4


title: mock-control-rep1


title: pooled clone sequencing from DNA cloning sample (ENCLB408UMW)

description:
https://www.encodeproject.org/experiments/ENCSR437KIU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR437KIU
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB408UMW


title: pooled clone sequencing from DNA cloning sample (ENCLB080ONU)

description:
https://www.encodeproject.org/experiments/ENCSR437KIU/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR437KIU
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB080ONU


title: antiSP1-dTAG-rep1


title: pooled clone sequencing from DNA cloning sample (ENCLB645CEM)

description:
https://www.encodeproject.org/experiments/ENCSR437KIU/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR437KIU
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB645CEM


title: antiSP1-dTAG-rep2


title: pooled clone sequencing from DNA cloning sample (ENCLB032SJV)

description:
https://www.encodeproject.org/experiments/ENCSR393KCY/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR393KCY
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB032SJV


title: Bulk, Hippocampus, Wildtype, rep3

city: Beijing

first: Magdalena

middle: Justyna

last: Koziol

address: Science Park Road

country: China

institute: Chinese Institute for Brain Researach, CIBR

data_processing:
For m6A-RIP: We required a minimum quality score of 5 at reads positions. adapters were removed using the software Cutadapt. Additionally, the first 10 nucleotides at the 5’ terminus were eliminated due to the presence of potentially low-quality nucleotides. Mapping and alignment were used by Hisat2, followed by peak calling using Macs2. To ensure reads unambiguously mapped in the genome, we further mapped the reads by bowtie2 alignment programs (The mapping parameters for bowtie2: -k 4, with other parameters in default setting.
For bulk-RNA-seq and m6A identification: Fastq files were filtered for low quality reads  and low quality bases were trimmed from the ends of the reads.  Bwa  was used to align the resulting reads. To identify C-to-T and m6A sites, we used an approach as described by Meyer et al. (Meyer, 2019).
For single cell RNA-seq and m6A identification: Filtered barcode matrices obtained from E-YTH and E-YTHmut single cell data were processed by Seurat. The software Bullseye was used to identify m6A sites in single cell sequencing data (Tegowski et al., 2022).
For single cell RNA-seq matrix files were generated
cims files were generated
Assembly: Mouse: mm39; HEK293T: hg38
Supplementary files format and content: For m6A-RIP: m6A peaks
Supplementary files format and content: For bulk-RNA seq: cims files
Supplementary files format and content: For single cell RNA-seq: matrix files

source_name: hippocampus

growth_protocol: Mice: Hippocampi were harvested from 3 month old mice. Animals were maintained and processed in accordance with CIBR guidelines. All experimental methods were approved and followed all regulations of the Welfare and Ethics Review Committee for Laboratory Animals. C57BL/6J mice were originally purchase from the Jackson Laboratory, but were made available through CIBR’s animal facility. For HEK293T cells: HEK293T cells were purchased from Beijing Xiehe Cell Bank and cultured at 37ºC with 5% CO2 in DMEM (Dulbecco's Modified Eagle Medium) containing 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
HEK293T cells were collected and RNA was extracted for downstream processing; For mouse hippocamus collections, hippocampi were dissected 2 weeks after AAV injectsions and RNA was extracted; for single cell analysis, cells were dissociated 2 weeks after AAV injections with using the Adult Brain Dissociation Kit (Miltenyi Biotex no. 130-107-677); for m6A-RIP, a pulldown was performed on RNA using the m6A antibody (Synaptic Systems, 202011), and a matching control input sample was keept.
for any bulk RNA seq: Sequencing libraries were generated from 1-10ng of total RNA from each replicate using the Single Cell Full Length mRNA kit and TruePrep® DNA Library Prep Kit V2 (Illumina), according to the manufacturer’s instructions. For single cell sequencing: Briefly, after hippocampi dissociation, cells were FACS sorted and EGFP positive were collected in ice-cold PBS containing 0.5% BSA. Per sample, 30,000 cells were loaded into a Rhapsody Cartridge (BD) and processed following the manufacturer’s instructions. Subsequently, single cell RNA sequencing libraries were prepared using the Rhapsody WTA kit (BD). For m6A-RIP: SMARTer Stranded Total RNA-Seq Kit v2 (Takara)
for single cells: Rhapsody WTA kit (BD); for bulk: TruePrep® DNA Library Prep Kit V2 (Illumina); for m6-RIP: SMARTer Stranded Total RNA-Seq Kit v2 (Takara)

treatment_protocol: Stereotaxic injections were performed on mice with AAV viruses; HEK293T cells were transduced;

value: hippocampus

value: wildtype

value: Wildtype


title: mNC_tumor 2

value: KRT14Cre+/-;Brd4loxp/wt; Nutm1loxp/wt


title: Single cell, Hippocampus, E-YTH

description: BDTM Rhapsody docker setup (BD)

value: E-YTH expressed


title: antiSP1-control-rep3

description:
antiSP1-control_merged_normalized.bigWig
antiSP1_ChIP_summits_final.bed


title: antiSP1-control-rep4


title: antiZNF143-dTAG-rep1


title: Single cell, Hippocampus, E-Mut

description: BDTM Rhapsody docker setup (BD)

value: E-Mut expressed


title: mNC_tumor 1


title: Bulk, Hippocampus, Wildtype, rep2


title: antiSP1-control-rep2


title: pooled clone sequencing from DNA cloning sample (ENCLB029WQZ)

description:
https://www.encodeproject.org/experiments/ENCSR393KCY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR393KCY
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB029WQZ

data_processing: See GSM*_README.txt supplementary file linked below

value: DNA cloning sample

value: cloning host


title: Bulk, Hippocampus, Wildtype, rep1


title: antiSP1-control-rep1


title: pooled clone sequencing from DNA cloning sample (ENCLB881OXP)

description:
https://www.encodeproject.org/experiments/ENCSR393KCY/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR393KCY
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB881OXP

value: synthetic construct

value: 60 days


title: Bulk, Hippocampus, E-YTH, rep3


title: Bulk, Hippocampus, E-YTH, rep2


title: Bulk, Hippocampus, E-YTH, rep1


title: pooled clone sequencing from DNA cloning sample (ENCLB950HPI)

description:
https://www.encodeproject.org/experiments/ENCSR335RIS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR335RIS
assay title: pooled clone sequencing
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB950HPI

value: Ryan Tewhey, JAX


title: Bulk, Hippocampus, E-Mut, rep3


title: pooled clone sequencing from DNA cloning sample (ENCLB335ZAL)

description:
https://www.encodeproject.org/experiments/ENCSR332LAV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR332LAV
assay title: pooled clone sequencing
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB335ZAL

value: not applicable


title: RNA-seq GFP rep 2

city: London

first: Duco

middle: Steven

last: Koenis

address: Charterhouse Square

department: William Harvey Research Institute

country: United Kingdom

institute: Queen Mary University of London

data_processing:
Raw sequencing reads were filtered for low complexity or repetitive sequences and aligned to the Mus musculus genome (assembly mm10, Dec. 2011) using TopHat 2.1 (Trapnell et al., 2009).
The number of uniquely mapping read counts per gene was determined using HTSeq (Anders et al., 2015).
Differential expression analysis between GFP and HA-NUR77 overexpressing cells was performed using DESeq2 (Love et al., 2014), wherein genes with a false discovery rate (FDR)-adjusted p-value < 0.05 and a log2(fold-change) < -0.3 or > 0.3 were considered to be differentially regulated.
Assembly: mm10
Supplementary files format and content: .txt files contain HTSeq counts of sequencing reads for each ENSEMBL transcript.

growth_protocol: C2C12 myoblast stable cell line with Dox-inducible overexpression of HA-NUR77 was seeded in one 10-cm dishes per replicate in DMEM medium supplemented with 10% fetal calf serum, 100 U/mL penicillin, 100 µg/mL streptomycin, and 2 mM L-glutamine.

extract_protocol:
Cells were lysed directly in plates and total RNA was extracted using TRIzol reagent (Invitrogen) according to manufacturer's instructions.
Strand-specific libraries were generated using the TruSeq Stranded mRNA Library Prep Kit (Illumina). Polyadenylated RNA from 1000 ng intact total RNA was purified using oligo-dT beads. Following purification, the RNA was fragmented, random primed and reverse transcribed using SuperScript II Reverse Transcriptase (Invitrogen). Second strand synthesis was performed using Polymerase I and RNase H with replacement of dTTP for dUTP. The generated cDNA fragments were 3' end adenylated and ligated to Illumina Paired-end sequencing adapters and subsequently amplified by 12 cycles of PCR. The libraries were analyzed on a 2100 Bioanalyzer using a 7500 chip (Agilent), diluted, and pooled in equimolar ratio into a 13-plex, 10 nM sequencing pool.

treatment_protocol: 24 hours after seeding, cells were treated with 1 µg/mL Doxycycline (Dox) for 18 hours.

tag: genetic modification

value: pINDUCER20b-GFP stable cell line

value: 1 µg/mL Dox for 18 hours


title: RNA-seq GFP rep 1


title: pooled clone sequencing from DNA cloning sample (ENCLB599XII)

description:
https://www.encodeproject.org/experiments/ENCSR332LAV/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR332LAV
assay title: pooled clone sequencing
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB599XII


title: Bulk, Hippocampus, E-Mut, rep2

tag: genotype


title: Bulk, Hippocampus, E-Mut, rep1

tag: treatment


title: RNA-seq HA-NUR77 rep 3

value: pINDUCER20b-HA-NUR77 stable cell line


title: pooled clone sequencing from DNA cloning sample (ENCLB614CPM)

description:
https://www.encodeproject.org/experiments/ENCSR332LAV/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR332LAV
assay title: pooled clone sequencing
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB614CPM

tag: biosample encode accession


title: RNA-seq HA-NUR77 rep 2


title: pooled clone sequencing from DNA cloning sample (ENCLB370GXW)

description:
https://www.encodeproject.org/experiments/ENCSR332LAV/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR332LAV
assay title: pooled clone sequencing
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB370GXW

tag: biosample term name


title: RNA-seq HA-NUR77 rep 1


title: Bulk, Hippocampus, E-APOBEC1, rep2

value: E-APOBEC1 expressed


title: pooled clone sequencing from DNA cloning sample (ENCLB549AJT)

description:
https://www.encodeproject.org/experiments/ENCSR332LAV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR332LAV
assay title: pooled clone sequencing
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB549AJT

tag: age


title: pooled clone sequencing from DNA cloning sample (ENCLB079WZU)

description:
https://www.encodeproject.org/experiments/ENCSR393KCY/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR393KCY
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB079WZU

tag: lab


title: C2C12 ChIP-seq HA-NUR77 rep1

data_processing:
Raw sequencing reads were aligned to the Mus musculus genome (assembly mm9, July 2007) using Burrow-Wheeler Aligner 0.7.10 (Li and Durbin, 2009). Reads that aligned poorly or mapped to multiple locations were discarded and only reads with a mapping quality score (MAPQ) over 20 were used for peak calling.
Raw input sequencing data for C2C12 cells was obtained from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database (accession number GSM1598795) and aligned and filtered as described above.
High-confidence Nur77 binding sites were identified by comparing aligned input and Nur77 ChIP-seq data using two peak calling algorithms, MACS (Zhang et al., 2008) and DFilter (Kumar et al., 2013). For MACS, default settings were used except for a p-value cut-off of 10^-7. For DFilter, the settings bs = 50, ks = 30, refine, and nonzero were used with a p-value cut-off of 10^-6.
Nur77 binding sites identified by both peak callers and present in at least two of the three biological replicates were used for further analyses.
Assembly: mm9
Supplementary files format and content: .bed files contain consensus peak calls from MACS and DFilter for each Nur77 ChIP-seq sample.
Supplementary files format and content: ChIPseq_C2C12_NUR77_mergedpeaks_mm9.bed contains peak calls that were present in at least 2 out of 3 biological replicates

growth_protocol: C2C12 myoblast stable cell line with Dox-inducible overexpression of HA-NUR77 was seeded in eighteen 15-cm dishes per replicate in DMEM medium supplemented with 10% fetal calf serum, 100 U/mL penicillin, 100 µg/mL streptomycin, and 2 mM L-glutamine.

extract_protocol:
Cells were washed with PBS and dual crosslinked directly in culture plates with 2 mM Di(N-succinimidyl) glutarate (Sigma) in PBS for 45 minutes at room temperature, followed by 1% formaldehyde (Sigma) for 15 minutes at room temperature. Crosslinking reactions were quenched by addition of glycine to 0.125 M final concentration and incubation for 5 minutes at room temperature. Crosslinked cells were washed with ice-cold PBS and collected by scraping in ice-cold PBS followed by centrifugation for 5 minutes at 500 x g. Cell pellets were resuspended  in resuspension buffer L1A (10 mM HEPES-KOH pH 7.9, 85 mM KCl, 1 mM EDTA). Cell membranes were lysed by diluting samples 1:1 with lysis buffer L1B (L1A plus 1% IGEPAL CA-630) and incubating 10 minutes on ice. Cells were subsequently centrifuged 5 minutes at 700 x g and pellets were resuspended in lysis buffer L2 (50 mM Tris-HCl pH 7.4, 1% SDS, 10 mM EDTA). Nuclei were ruptured and chromatin was sonicated into approximately 200 bp fragments using a Bioruptor Pico (Diagenode) for 20 cycles of 30 seconds on and 30 seconds off. Fragment length was confirmed by running an aliquot of reverse crosslinked chromatin on a 1.2% agarose gel. Sonicated chromatin samples were centrifuged for 10 minutes at 16,000 x g to pellet cell debris. Supernatants were transferred to DNA LoBind tubes (Sigma) and diluted 1:1.5 with dilution buffer (20 mM Tris-HCl pH 7.4, 100 mM NaCl, 2 mM EDTA, 0.5% Triton X-100). Per ChIP reaction, 30 µL Protein G Dynabeads (Novex) were washed twice with 0.5% bovine serum albumin (BSA) in PBS and incubated with 2 µg anti-HA antibody (Diagenode) for 3 hours at 4°C. Dynabead-antibody complexes were added to each diluted chromatin sample (18 ChIPs total) and incubated overnight at 4°C to immunoprecipitate chromatin-linked HA-NUR77 protein. Immunoprecipitates were washed four times with wash buffer 1 (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA), four times with wash buffer 2 (10 mM Tris-HCl pH 7.4, 250 mM LiCl, 1% IGEPAL CA-630, 0.7% sodium deoxycholate, 1 mM EDTA), twice with wash buffer 3 (10 mM Tris-HCl pH 7.4, 0.2% Triton X-100, 1 mM EDTA), and twice with wash buffer 4 (10 mM Tris-HCl pH 7.4, 50 mM NaCl, 1 mM EDTA). Samples were transferred to fresh DNA LoBind tubes after the first and second to last wash steps to reduce background. Chromatin was eluted from Dynabeads by incubating in elution buffer (10 mM Tris-HCl pH 7.4, 2% SDS, 1 mM EDTA) for 20 minutes at 37°C. Crosslinks were reversed by addition of NaCl to a final concentration of 300 mM and incubating overnight at 65°C. DNA was purified by incubating samples with 0.33 mg/mL RNase A for 1 hour at 37°C, followed by 0.5 mg/mL Proteinase K for 1 hour at 50°C, and extraction of DNA by phenol:chloroform:isoamylalcohol precipitation. Precipitated DNA was dissolved in ultrapure water and DNA from 6 separate ChIP reactions was pooled to create one biological replicate, resulting in three biological replicates total.
ChIP DNA libraries were prepared as previously described (Schmidt et al., 2009; PMID: 19275939).

tag: chip antibody

value: Rabbit-anti-HA antibody (Millipore)


title: pooled clone sequencing from DNA cloning sample (ENCLB391EDL)

description:
https://www.encodeproject.org/experiments/ENCSR205HWY/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR205HWY
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB391EDL

tag: Sex


title: C2C12 ChIP-seq HA-NUR77 rep2

tag: cell line


title: Bulk, Hippocampus, E-APOBEC1, rep1

value: hippocampus

tag: strain


title: RNA-seq GFP rep 3


title: pooled clone sequencing from DNA cloning sample (ENCLB124ODZ)

description:
https://www.encodeproject.org/experiments/ENCSR393KCY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR393KCY
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB124ODZ


title: T1D_Patient_8_RNA_EdgeSeq

city: Boston

first: Eiichiro

last: Satake

state: MA

address: One Joslin Place

department: Genetics and Epidemiology

institute: Joslin Diabetes Center

data_processing:
For edgeSeq, the sequencing data were imported into HTG EdgeSeq Parser software to align the FASTQ files obtained from the sequencer to miRBase v.21 sequences.
For RNASeq_1, data were analyzed using a SeqMatic in-house pipeline that included initial processing and demultiplexing using Illumina’s CASAVA v1.8.2 software pipeline
For RNASeq_2, small RNA sequencing data were analyzed using ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, low complexity, common RNA families and repeats. Unique sequences with length in 18-26 nucleotide were then mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Assembly: miRBase v21
Supplementary files format and content: tab-delimited text file include raw counts for each sample
Supplementary files format and content: tab-delimited text file include normalized CPM counts for each platform

source_name: plasma

extract_protocol:
For the edgeSeq and RNASeq_1, total RNA was isolated from the selected samples using 180 µl of plasma from each individual and Qiagen’s miRNeasy Serum/Plasma kit (QIAGEN, Valencia, CA) according to the manufacturer’s protocol as previously published.
For small RNASeq performed by RNASeq_2, total RNA was extracted by the company from 200 ml of plasma using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure.
For the edgeSeq, the library was prepared using HTG EdgeSeq PCR processing and quantified using HTG EdgeSeq KAPA Library Quantification for Illumina Sequencing.
For RNASeq_1, SeqMatic’s TailorMix miRNA Sample Preparation Kit V2 was used according to the manufacturer’s recommendations
For RNASeq_2, total RNA was used to prepare small RNA libraries using the commercially available TruSeq Small RNA Sample Prep Kit (Illumina, San Diego, USA) according to the manufacturer’s protocol.

value: plasma


title: pooled clone sequencing from DNA cloning sample (ENCLB740GKP)

description:
https://www.encodeproject.org/experiments/ENCSR205HWY/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR205HWY
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB740GKP


title: Hippocampus, m6A RIP-pulldown, rep3

data_processing:
For m6A-RIP: We required a minimum quality score of 5 at reads positions. adapters were removed using the software Cutadapt. Additionally, the first 10 nucleotides at the 5’ terminus were eliminated due to the presence of potentially low-quality nucleotides. Mapping and alignment were used by Hisat2, followed by peak calling using Macs2. To ensure reads unambiguously mapped in the genome, we further mapped the reads by bowtie2 alignment programs (The mapping parameters for bowtie2: -k 4, with other parameters in default setting.
For bulk-RNA-seq and m6A identification: Fastq files were filtered for low quality reads  and low quality bases were trimmed from the ends of the reads.  Bwa  was used to align the resulting reads. To identify C-to-T and m6A sites, we used an approach as described by Meyer et al. (Meyer, 2019).
For single cell RNA-seq and m6A identification: Filtered barcode matrices obtained from E-YTH and E-YTHmut single cell data were processed by Seurat. The software Bullseye was used to identify m6A sites in single cell sequencing data (Tegowski et al., 2022).
For single cell RNA-seq matrix files were generated
cims files were generated
Assembly: Mouse: mm39; HEK293T: hg38
Supplementary files format and content: For m6A-RIP: m6A peaks
Supplementary files format and content: For bulk-RNA seq: cims files
Supplementary files format and content: For single cell RNA-seq: matrix files
Library strategy: m6A RIP-Seq

value: wildtype

value: m6A RIP pulldown


title: Hippocampus, m6A RIP-input, rep3

value: m6A RIP input control


title: pooled clone sequencing from DNA cloning sample (ENCLB403MQT)

description:
https://www.encodeproject.org/experiments/ENCSR205HWY/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR205HWY
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB403MQT


title: T1D_Patient_7_RNA_EdgeSeq


title: Hippocampus, m6A RIP-pulldown, rep2


title: pooled clone sequencing from DNA cloning sample (ENCLB155HME)

description:
https://www.encodeproject.org/experiments/ENCSR205HWY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR205HWY
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB155HME


title: Hippocampus, m6A RIP-input, rep2


title: Bulk, Hippocampus, E-APOBEC1, rep3


title: C2C12 ChIP-seq HA-NUR77 rep3


title: T1D_Patient_6_RNA_EdgeSeq


title: T1D_Patient_4_RNA_EdgeSeq


title: pooled clone sequencing from DNA cloning sample (ENCLB604QEV)

description:
https://www.encodeproject.org/experiments/ENCSR205HWY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR205HWY
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB604QEV


title: T1D_Patient_3_RNA_EdgeSeq


title: Hippocampus, m6A RIP-pulldown, rep1


title: pooled clone sequencing from DNA cloning sample (ENCLB554OHP)

description:
https://www.encodeproject.org/experiments/ENCSR020JTL/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR020JTL
assay title: pooled clone sequencing
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB554OHP


title: pooled clone sequencing from DNA cloning sample (ENCLB142UWI)

description:
https://www.encodeproject.org/experiments/ENCSR152PLX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR152PLX
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB142UWI


title: pooled clone sequencing from DNA cloning sample (ENCLB573TIT)

description:
https://www.encodeproject.org/experiments/ENCSR020JTL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR020JTL
assay title: pooled clone sequencing
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB573TIT


title: Hippocampus, m6A RIP-input, rep1


title: T1D_Patient_1_RNA_EdgeSeq


title: pooled clone sequencing from DNA cloning sample (ENCLB223LAS)

description:
https://www.encodeproject.org/experiments/ENCSR020JTL/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR020JTL
assay title: pooled clone sequencing
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB223LAS


title: P1, microglia, developing cortex, replicate 2

city: Cambridge

first: Paola

last: Arlotta

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 and v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Developing microglia atlas samples were further processed with the Kallisto | Bustools pipeline (https://www.kallistobus.tools/)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: S1 cortex

extract_protocol:
For single-cell microglia isolates: Somatosensory (S1) cortex was dissected and meninges removed. S1 cortex blocks were minced and pelleted at 500g for 5 minutes. The pellet was resuspended in 1mL dissociation buffer (20mL PBS + 20uL RNasin + 400uL DNAse). The tissue was homogenized with 15 plunges of pestle "A" and passed through a 70um cell strainer, and pelleted at 500g for 5 minutes. The pellet was resuspended in 500uL FACS buffer (PBS with 0.04% BSA). Cells were labelled with anti-Cd11b-PE, anti-Cx3cr1-APC, and anti-Cd45-APC/Cy7, and FACS sorted to isolate microglia.
Libraries were prepared according to manufacturer's insctructions using Chromium Single Cell 3' Kit v3.1 (10X Genomics, PN-1000121).

tag: cell type

value: microglia

value: S1 cortex

value: Mixed

value: WT


title: T1D_Patient_7_plasma_EdgeSeq

library_source: other

molecule: other


title: T1D_Patient_8_plasma_EdgeSeq


title: P1, microglia, developing cortex, replicate 1

description: 10X Genomics

tag: developmental stage


title: E18, microglia, developing cortex, replicate 1

description: 10X Genomics


title: NPC1KO female mice FC 1

city: Richmond

first: Vikas

middle: A

last: Gujjala

state: Virginia

address: 1000 W Cary Street

department: Biology

institute: Virginia Commonwealth University

data_processing:
Hisat2 v2.0.5 was used to align reads to reference genome (mm39)
featureCounts was used to quantify reads
DESeq2 R package was used to calculate differential gene expression
Assembly: mm39
Supplementary files format and content: excel file includes differentially expressed genes for female or male NPC1KO vs WT mice samples
Supplementary files format and content: excel file includes raw counts for each sample
Supplementary files format and content: excel file includes fpkm counts for each sample

source_name: frontal cortex brain samples

extract_protocol:
Total RNA from frontal cortex brain samples was used. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads.
Using purified mRNA, after fragmentation, The first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis

value: frontal cortex brain samples

value: NPC1 KO

value: female


title: NPC1KO female mice FC 3


title: E16, microglia, developing cortex, replicate 1

description: 10X Genomics


title: T1D_Patient_5_plasma_EdgeSeq


title: NPC1KO female mice FC 2


title: E18, microglia, developing cortex, replicate 2

description: 10X Genomics


title: E15, microglia, developing cortex, replicate 2

description: 10X Genomics


title: T1D_Patient_5_RNA_EdgeSeq


title: T1D_Patient_2_RNA_EdgeSeq


title: T1D_Patient_3_plasma_EdgeSeq


title: T1D_Patient_4_plasma_EdgeSeq


title: E15, microglia, developing cortex, replicate 1

description: 10X Genomics


title: NPC1KO male mice FC 2

value: male


title: wildtype female mice FC 3


title: E14, microglia, developing cortex, replicate 1

description: 10X Genomics


title: E14, microglia, developing cortex, replicate 2

description: 10X Genomics


title: E13, microglia, developing cortex, replicate 2

description: 10X Genomics


title: wildtype female mice FC 2


title: T1D_Patient_1_plasma_EdgeSeq


title: T1D_Patient_6_plasma_EdgeSeq


title: MPRA from K562 (ENCLB779CZY)

description:
https://www.encodeproject.org/experiments/ENCSR971BEX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR971BEX
assay title: MPRA
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB779CZY
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000

source_name: Homo sapiens K562 cell line genetically modified (episome) using transient transfection, 48 hours post-nucleic acid delivery time

tag: line

value: cell line

tag: collection date

value: not applicable

tag: geographic location

tag: encode accession

tag: health state

value: chronic myelogenous leukemia (CML)

tag: dev stage

value: adult

value: 53 years

tag: passage number

value: Ryan Tewhey, JAX

tag: source

value: ATCC

tag: link

value: ENCBS510CSS at ENCODE; https://www.encodeproject.org/ENCBS510CSS/


title: E13, microglia, developing cortex, replicate 1

description: 10X Genomics

tag: tissue

tag: genotype


title: wildtype male mice FC 3


title: wildtype female mice FC 1


title: NPC1KO male mice FC 3


title: MPRA from K562 (ENCLB573DEC)

description:
https://www.encodeproject.org/experiments/ENCSR971BEX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR971BEX
assay title: MPRA
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB573DEC
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000

tag: biosample encode accession

tag: age

tag: lab

value: ENCBS901KAO at ENCODE; https://www.encodeproject.org/ENCBS901KAO/


title: wildtype male mice FC 2

tag: Sex


title: E12, microglia, developing cortex, replicate 1

description: 10X Genomics

tag: cell type

value: microglia

tag: strain


title: MPRA from HepG2 (ENCLB330WWV)

description:
https://www.encodeproject.org/experiments/ENCSR811QES/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR811QES
assay title: MPRA
possible controls: ENCSR441MQR
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB330WWV
fragmentation methods: none

source_name: Homo sapiens HepG2 cell line genetically modified (episome) using transient transfection, 24 hours post-nucleic acid delivery time

tag: line

value: hepatocellular carcinoma

value: child

value: 15 years

value: ENCBS090QIG at ENCODE; https://www.encodeproject.org/ENCBS090QIG/


title: NPC1KO male mice FC 1

value: frontal cortex brain samples

value: NPC1 KO


title: MPRA from HepG2 (ENCLB924ISU)

description:
https://www.encodeproject.org/experiments/ENCSR811QES/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR811QES
assay title: MPRA
possible controls: ENCSR441MQR
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB924ISU
fragmentation methods: none

tag: collection date

value: male

value: ENCBS556FBL at ENCODE; https://www.encodeproject.org/ENCBS556FBL/


title: T1D_Patient_2_plasma_EdgeSeq

value: plasma


title: S1 cortex, Csf1r KO, poly(I:C), replicate 2

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: snRNA-seq

molecule: nuclear RNA

extract_protocol:
For single-cell microglia isolates: Somatosensory (S1) cortex was dissected and meninges removed. S1 cortex blocks were minced and pelleted at 500g for 5 minutes. The pellet was resuspended in 1mL dissociation buffer (20mL PBS + 20uL RNasin + 400uL DNAse). The tissue was homogenized with 15 plunges of pestle "A" and passed through a 70um cell strainer, and pelleted at 500g for 5 minutes. The pellet was resuspended in 500uL FACS buffer (PBS with 0.04% BSA). Cells were labelled with anti-Cd11b-PE, anti-Cx3cr1-APC, and anti-Cd45-APC/Cy7, and FACS sorted to isolate microglia. For single-nucleus S1 cortex samples from Csf1r null and WT mice: Prospective S1 cortices of E15.5 embryos were dissected and flash-frozen in liquid nitrogen and stored at -80C. Frozen tissue blocks from male Csf1r mutant and WT embryos were processed to obtain a single-cell suspension using papain digestion (15 minutes) (Papain dissociation kit, Worthington), following the manufacturer’s protocol. After dissociation and concentration, the pellet was resuspended in 500 uL of Nuclei Solubilization Buffer (10 mL PBS (Gibco, 15630-080) + 50 uL of 20 mg/mL BSA (NEB, B9000S) + 10 uL RNasin (Promega, N26515)) spiked with 1 uL of Hoechst and passed through a 40 um filter (Corning 352235). Nuclei were sorted on a Beckman Coulter MoFlo Astrios EQ Cell Sorter, pre-chilled to 4C, using a 100 um nozzle, and collected into wells of a 96-well plate pre-filled with 10 uL of Nuclei Solubilization Buffer, and immediately processed for single-cell GEM formation (10x Genomics, single cell RNA sequencing 3’, Chromium v3.1).
Libraries were prepared according to manufacturer's insctructions using Chromium Single Cell 3' Kit v3.1 (10X Genomics, PN-1000121).

treatment_protocol: Mothers were given intraperitoneal injections at E12.5 of either poly(I:C) to induce maternal immune activation, or saline as a control.

value: S1 cortex

value: Male

tag: developmental stage

tag: treatment


title: S1 cortex, Csf1r KO, nacl, replicate 2

description: 10X Genomics

value: saline


title: wildtype male mice FC 1

value: WT


title: S1 cortex, WT, poly(I:C), replicate 2

description: 10X Genomics


title: MPRA from HepG2 (ENCLB286LSO)

description:
https://www.encodeproject.org/experiments/ENCSR811QES/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR811QES
assay title: MPRA
possible controls: ENCSR441MQR
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB286LSO
fragmentation methods: none

value: cell line

value: not applicable

tag: geographic location

tag: encode accession

tag: health state

value: Ryan Tewhey, JAX

value: ATCC

value: ENCBS685NCZ at ENCODE; https://www.encodeproject.org/ENCBS685NCZ/